If the Dark Apprentice had any reason to believe that he was the real Starkiller who defeated Vader and saved the Rebellion, he might start to reconsider his decisions, kind of like a kid who's been told all his life that he's adopted only to discover that he was kidnapped. Believing that the real Starkiller truly died would also grant him some humility and maybe even warn him about the consequences of betraying Vader. (Yes, I just speculated that the Dark Apprentice could be the real Marek.)

It would seem that the very existence of the Dark Apprentice makes it far more likely that Starkiller is a clone, but I'm still holding on to a spark of hope that he isn't.

Edit:

It would appear from her odd behavior, her survival of a fatal fall, and Vader's last words that the new Juno is fake (from "micksith" on LucasArts forum). So what does this have to do with our debate? Just a thought - it seems like Vader is going all out to recover this one clone - he even wants to take him alive. Why would he go to so much trouble for a clone if he has the body and a "perfect" copy of it in his pocket already?

In the databank, a cloning facility employee complains about not having the original body to inspect.